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Guest Student Programme 2004


Esser, Rüdiger (Hrsg.) (2004)
 Beiträge zum Wissenschaftlichen Rechnen - Ergebnisse des Gaststudentenprogramms 2004 des John von Neumann-Instituts für Computing (PDF, 2 MB)
Technical Report IB-2004-11, 2004


Fast Near-Neighbour Search in Molecular Dynamics Simulation Using a Hashed Oct Tree

Nikos Elpidoforou, University of Athens, Greece
Adviser: Paul Gibbon

The traditional near-neighbour searches in MD codes require an O(N) computational effort per particle. Tree Algorithms can reduce this to O(logN) exploiting the tree structure to obtain an initial list of neighbour 'boxes'. The aim of this article is to explore a fast near-neighbour search algorithm based on the Hashed Oct Tree data structure. The particle coordinates are mapped onto a sorted list of binary keys, which can be used to determine rapidly the location of the particles within the tree. The introduced algorithm is exploiting the properties of the particle keys to create a near-neighbour list.

The Estimation of Charge Extensions in the Continuous Fast Multipole Method (CFMM)

Ivo Kabadshow, Chemnitz University of Technology
Adviser: Holger Dachsel

The Fast Multipole Method is advantageous, if one wants to examine large numbers of particles because of its scaling. However, generalizing this method to continuous charges, correspondingly called Continuous Fast Multipole method, leads to new problems. Especially the treatment of the arising non-zero extents must be studied carefully. For s-type distributions one can calculate the extent analytically. However, such an analytical solution does not exist for higher angular momenta. For that reason one has to estimate an upper bound for these extents that reflects the real extent very well since it affects the performance of the Continuous Fast Multipole Method.

Quantum Chemical Investigations on the Auger Process Induced Fragmentation of Organic Compounds and its Significance to DNA Irradiation Damage

Slawomir Pitula, Jonas Wiebke, University of Cologne, Dept. of Chemistry
Adviser: Thomas Müller

125I transforms to highly excited 125Te via electron capture, leaving core shell vacancies that result in massive Auger emission. Molecular systems incorporating 125I will, following the 125I decay, fragment into molecular and atomic positive ions with individual charges of up to +18, a process commonly referred to as "Coulomb explosion". Auger emitters are highly radiotoxic, and have been subject to radiomedical research for decades. Whereas the investigation of the effects of Auger processes on biological systems could improve the understanding of basic aspects of radiotoxicity in general, 125I Auger electron emission may play a pioneering role in therapeutical applications, such as tumor-specific radionuclide deposition.

However, there is still much uncertainty in the molecular and cellular mechanisms following Auger processes in vivo. In this work, the response of a 77Br-substituted 10 base pair DNA sequence on excessive ionization was investigated by quantum chemical methods on a DFT level of theory. Here and in further systems 77Br was chosen as the Auger emitter instead of 125I, to overcome certain problems as discussed below. In a first approach, the Coulomb explosion of CH3125I, C2H5125I, and n-C3H7125I was studied systematically to draw connections between electronic structures and observed fragmentation patterns. This was done by considering the Auger electron emission as being finished, and calculating the nuclear relaxation for the electronic ground state of the molecular ions. More calculations were carried out on the Coulomb explosion of 125Iodouracil, 77Bromouridine-5'-monophosphate, and the 77Bromouridine-5'-monophosphate-Adenosine-5'-monophosphate nucleotide pair.

NMR-Quantum Computer Simulation on a Parallel Supercomputer

Nikolas Pomplun, Technical University of Berlin
Adviser: Guido Arnold, Marcus Richter

The aim of this work was to simulate the time evolution of a quantum computer system. The simulation code was optimized to run on a parallel computer that provides the needed resources to model the time evolution in a reasonable time. Thereby the attention was focused on two major features. First the Suzuki-Trotter algorithm that was used to model the time evolution and second the adjustment to a specific realisation of such a computer: the Nuclear Magnetic Resonance Quantum Computer.

Fast Parallel Matrix Multiplication: The Strassen - Winograd Algorithm

Armin Rund, Universität Bayreuth
Adviser: Bernhard Steffen

This article describes different approaches to speed up matrix-matrix multiplications. In the serial case three algorithms are compared. An optimized assembler code is combined with the serial and parallel algorithms. A concept for parallel matrix-matrix multiplication is discussed.

Visualisierung von MHD-Daten mit Virtual-Reality-Techniken

Sebastian Schiffner, Freie Universität Berlin
Adviser: Herwig Zilken

Ziel der Arbeit war es, ein OpenGL Programm zur Visualisierung von Magneto-Hydro-Dynamischen Vorgängen im Erdinneren zu erweitern. Die Aufgabenstellung fing mit einfachen Dingen, wie einer flexibleren Isolinien-Darstellung an und steigerte sich dann mit einer Isoflächenanzeige mittels des Marchingcube Algorithmus, interaktiver Steuerung durch das Trackingsystem 3Space Fastrak von Polhemus und zum Schluss der Dreidimensionalisierung der Anzeige durch das Verwenden von zwei Framebuffern. Im Folgenden wird näher auf einige Besonderheiten eingegangen die es zu beachten gibt beim Umgang mit Virtual-Reality Techniken.

A Parallel Cluster Algorithm for Monte Carlo Simulations Applied to Model DNA Systems

Jakob Schluttig, Institute for Theoretical Physics University of Leipzig
Adviser: Godehard Sutmann

Cluster methods are used in Monte Carlo simulations to decrease the autocorrelation time, i.e. the interval between statistically independent configurations, which becomes crucial close to critical points and phase transitions. The aim of this work is to build the basis for a Monte Carlo cluster algorithm for continuous two dimensional spin systems. First the Kornyshev-Leikin model potential is introduced which is applied to Monte Carlo simulations of DNA systems. Afterwards a purely geometrical technique for searching clusters is described. Furthermore it is extended to an energetic cluster criterion, which is the basis in Monte Carlo cluster methods. The scaling of the implementation is measured and analyzed. Finally it is used to study geometric clusters as a function of different DNA characteristics, e.g. the charge compensation parameter θ.

Resource Negotiation in Unicore: The Web Services Agreement Approach

Jiulong Shan, National High Performance Computing Center (Hefei China)
Adviser: Volker Sander

UNICORE, a popular Grid Computing software, facilitates the seamless and secure sharing of computing powers among distributed supercomputers. In its current implementation, UNICORE adopts a static resource management model which can not fully meet the user's requirement on resource provisioning. In this work, we propose the incorporation of a Web services (WS) Agreement based resource negotiation model to advance the current resource management model of UNICORE. The feasibility of the proposed approach is validated through experiments based on a prototype implementation.

Group Photo

Guest Students 2004Guest students and trainees 2004 with some of their advisers

Persons on the photo, left to right, front to back:

1. row: Rüdiger Esser (ZAM), Bernhard Steffen (ZAM), Jiulong Shan (Hefei, China), Ivo Kabadshow (Chemnitz), Sebastian Schiffner (Berlin), Inge Gutheil (ZAM)
2. row: Holger Dachsel (ZAM), Slawomir Pitula (Köln), Nikos Elpidoforou (Athen), Annika Günther (Aachen)
3. row: Jonas Wiebke (Köln), Jakob Schluttig (Leipzig), Armin Rund (Bayreuth), Herwig Zilken (ZAM)
4. row: Benjamin Sohn (Dresden), Nikolas Pomplun (Berlin), Godehard Sutmann (ZAM)